Field of Science

Just When You Thought It Was Safe

Smalltooth cookiecutter shark Isistius brasiliensis, photographed by Joshua Lambus.

Sometimes, you can get pretty much everything you need to know from the title of an article alone. To whit:
First documented attack on a live human by a cookiecutter shark (Squaliformes, Dalatiidae: Isistius sp.)
The article itself is in a journal I don't have access to, but I can read the abstract: the person attacked was a long-distance swimmer in Hawaii and was bitten twice. The bite was treated with skin grafts, but still took nine months to finish healing.

Cookiecutter sharks are one of the more fascinatingly evil fish out there. They are small, as sharks go (up to about 50 cm, tops) but have proportionately oversized teeth that are arranged in a tight, single-row array that can be protruded outwards to take a neat plug out of the flesh of a larger animal: hence the name of 'cookiecutter'. The effectiveness of the cutting tooth row is maintained by being replaced all at once, rather than individual teeth being replaced piecemeal as in other sharks. Cookiecutters are rarely encountered by humans as they are generally deep sea fish, living below the light zone, but like many mesopelagic animals they appear to migrate closer to the surface at night (Papastamatiou et al. 2010). Bioluminescent photophores behind the head have been suggested to function as a lure, drawing larger fish, dolphins, etc. into range of an ambush. Cookiecutters have very catholic tastes, and evidence of bites has been recorded from just about any decent-sized pelagic animal. They will even bite the external insulation on submarines.

Fish with cookiecutter bites, from Rick Macpherson (who, it turns out, covered this event when it was first happened).

Given their lack of pickiness, it is hardly surprising that a cookiecutter would take a bite out of a human. Of course, humans very rarely venture into the pelagic environment in which cookiecutters can be found. The very fact that the Hawaii indicent is the first confirmed attack indicates how extremely rare this would be expected to be. The Wikipedia page on cookiecutters refers to possible attacks on shipwreck survivors (though the source page linked to does not provide citations for such reports), and the body of a drowned fisherman was recovered in Hawaii with cookiecutter bites. But unless you happen to be swimming in the open ocean at night, your chances of being bitten by a cookiecutter are low.


Papastamatiou, Y. P., B. M. Wetherbee, J. O’Sullivan, G. D. Goodmanlowe & C. G. Lowe. 2010. Foraging ecology of cookiecutter sharks (Isistius brasiliensis) on pelagic fishes in Hawaii, inferred from prey bite wounds. Environmental Biology of Fishes 88 (4): 361-368.

The Overwhelming Diversity of Life

A post yesterday at Pharyngula has referred to a series of dinosaur parks in the United States that put up an information page on their website revealing a creationist agenda. As I've noted before, I tend not to concern myself with the activities of creationists because I generally find them exceedingly dull (I'm often tempted to repurpose a line spoken by Julian Rhind-Tutt in an episode of Green Wing: "You know what? The rest of us have moved on."). However, my eye was caught by one line that reflects on one of the major misunderstandings involved. In the process of postulating how dinosaurs became extinct subsequent to the Flood:

It is not just dinosaurs that have become extinct. In the last 350 years alone, almost 400 species have disappeared.

For various numbers, the total of '400 species' is probably severely underestimated, but that's not what I want to focus on. Instead, I want to look at the number itself. If there is one thing that most people fail to grasp about biodiversity, it would be that there's just so much of it. It's an understandable failing: I work with biodiversity on a daily basis, and even I find myself constantly startled and awed by this point. So huge are the numbers involved that it's almost counter-productive to simply report them. Humans seem to have a tendency to effectively just lump any number over a hundred or so as simply 'a lot'.

Imagine you were an avid twitcher (one with an enthusiasm for seeing new bird species) who, through a preternatural combination of flawless logistics, limitless funding and exceptional luck, was able to observe one new bird every day. At that rate, how long would it take you see every species of bird in the world? Wikipedia gives a figure of about 10,000 species of bird, which would mean that you would need 27 years, four months and 25 days. If you started at the age of 18, you would not finish until after your 45th birthday. If you moved on to mammals, you would need another fifteen and a half years. Lizards would account for another ten years; snakes another eight. Turtles you would be able to get through in just under a year, but then frogs would require thirteen and a half. Fish, on the other hand, would require the investment of some seventy years. Or, to sum up, observing every known living species of vertebrate at the rate of one a day would require nearly twice as much time as most of us are allotted in a single lifespan.

Outside vertebrates, the numbers just keep adding up. Earthworms may not seem like a hugely diverse group, but would still require an investment of more than sixteen years. You'd need more than 126 years to get through the staphylinid beetles alone. Perhaps plants are more your thing? You'd better have dedication, then: it's going to take you nearly 700 years if you want to see every variety of flower in the world. After that, the mere 33 years required to deal with the ferns will just go by in a flash.

No-one has yet tallied up exactly how many species of organism have been described to date, but using a conservative (very conservative) estimate of 1.5 million, observing every one at the rate of one species a day would take you more than 4100 years. Or 45 somewhat generous life spans (assuming, of course, that you were able to get things started from the day of your birth). Compared to this, 400 species is but a drop.

It was no accident that the concept of evolution achieved its majority in the nineteenth century. Naturalists at that time were required more and more to come to terms with just how diverse the world's organisms were, and how inadequate the popular explanations were in accounting for such diversity. What is one supposed to make of a god who would apparently bless to the world with over a thousand species of tapeworm? Or over 100 species of scabies mite? Unless, of course, we should simply take it as evidence that God has an inordinate fondness for scabies.

The August History of Filter-Feeding Ostracods

Today's post subject, the Cavellinidae, were a family of ostracods that were around from the Middle Silurian period to the Middle Triassic (Adamczak 2003a). And for those of you unfamiliar with ostracods: you lucky, lucky bastards. They're horrible.

I exaggerate slightly. Ostracods are a group of crustaceans that spend their lives enclosed in a pair of shells, superficially a bit like a bivalve, However, what they primarily are is very, very small (often less than a millimetre in total length), which makes them very difficult to work with as identification often requires dissecting out the (even smaller, needless to say) appendages hidden within the shells. Fortunately, I've personally managed so far to avoid being caught in ostracod purgatory, but many of my acquaintances have not been so fortunate. In the case of fossil ostracods like today's subjects, it is generally only the valves themselves and not any of the internal parts that are preserved to be of concern, but they're still small enough overall to hardly be counted as simple to work with.

External dorsal and lateral views of the carapace of each sex of the Silurian Gotlandella martinssoni, from Adamczak (2003a) (adr = admarginal ridge, mr = marginal ridge).

Cavellinids belong to a group of ostracods called the Platycopina, so-called because of their relatively flat sides. Among the modern fauna, platycopines are represented only by the genus Cytherella, whose distant ancestors were almost certainly among the species assigned to the Cavellinidae (Adamczak 2003a), so the 'extinction' of the cavellinids in the Triassic is really a pseudo-extinction as they were replaced by the descendant cytherellids. As befits its phylogenetic isolation from other living ostracods, Cytherella is an oddity in the modern fauna, being one of the few ostracod lineages to make a living as filter-feeders. The rear part of the carapace is expanded on the inside to form a brood chamber in which the eggs are nursed. It has been suggested that the evolution of filter-feeding and of the brood chamber were connected (Adamczak 2003b): as water is drawn in by the process of filter-feeding, it circulates around the brood chamber to keep the contents, whether eggs or newly hatched larvae, oxygenated. The constant flow of water also brings more oxygen to the adult's own gills than it would receive passively, so Cytherella are able to live in places with less dissolved oxygen than other ostracods (Lethiers & Whatley 1994).

Internal view of right valve of the Middle Devonian Birdsallella eifeliensis, from Adamczak (2003a). Abbreviations: cg = contact groove (where the left valve is nestled); li = limen (the inner partition separating off the probable brood chamber).

Though preserved appendages have not yet been recorded from any cavellinid, their valve morphology is very similar to that of Cytherella: closely sized valves (the right is only slightly larger and slightly overlapping the left), with the line of contact between the valves is fairly straight along the underside, and the valves gaping open slightly at the front but tightly closed towards the back. A constriction on the inside of the valve also indicates the presence of a Cytherella-like brood chamber, and like Cytherella the outer surface of the carapace is fairly smooth. In fact, the only really marked difference between cavellinids and cytherellids is the arrangement of the muscle scars indicating where the valves where held together: in Cytherella and fossil members of the Cytherellidae, the scars are arranged in a double row, while members of the Cavellinidae have the scars in a random cluster. Because of the similarities between cavellinids and Cytherella, it is inferred that cavellinids were also filter feeders. Filter-feeding ostracods seem to have been more diverse in the Palaeozoic than in the present, leading Lethiers & Whatley (1994) to suggest that the Palaeozoic marine environment may have contained lower oxygen levels in many places than the modern environment. However, this line of reasoning was dismissed by Becker (2005), who felt that there was no reason to assume that fossil filter-feeders would necessarily show the same preference for low-oxygen environments as modern Cytherella. Instead, Becker has argued that strongly calcified ostracods like cavellinids are indicative of relatively high energy environments in shallow coastal waters (Adamczak 2003a).


Adamczak, F. J. 2003a. The platycopine dynasty 2. Family Cavellinidae Egorov, 1950. Authentic platycopines. N. Jb. Geol. Paläont. Abh. 229 (3): 375-391.

Adamczak, F. J. 2003b. The early platycopine dynasty (Ostracoda; Palaeozoic). Senckenbergiana Lethaea 83 (1-2): 53-59.

Becker, G. 2005. Functional morphology of Palaeozoic ostracods: phylogenetic implications. Hydrobiologia 538: 23-53.

Lethiers, F., & R. Whatley. 1994. The use of Ostracoda to reconstruct the oxygen levels of Late Palaeozoic oceans. Marine Micropaleontology 24 (1): 57-69.

Saddling the Truffles

The black elfin saddle Helvella lacunosa, photographed by Fred Stevens.

The subject of today's post is the fungus family Helvellaceae. In the past, the Helvellaceae have been treated as the family including the morels and false morels. False morels and morels are ascomycetes* that produce convoluted fruiting bodies generally supported above ground by a stalk. However, molecular analyses have unanimously indicated the non-monophyly of the morels and false morels relative to the truffles (Percudani et al. 1999), which produce their fruiting bodies underground (while above-ground fungi have their spores generally dispersed by the wind, truffles have spores dispersed by passing through an animal's digestive system after it eats the truffle). The intermingled relationship between truffles and morels had already been indicated by morphologists based on microscopic features of the spores and asci, and so past members of the Helvellaceae have been dispersed among multiple families. At the same time, genera of truffles have been shown to have a relationship with the Helvellaceae, so of the five genera listed in Helvellaceae in the most recent "Outline of Ascomycota" (Lumbsch & Huhndorf 2007) only two (Helvella and Cidaris) are above-ground fruiters, while the other three (Balsamia, Barssia and Picoa) are truffles. This is ignoring the point that the single known species of Cidaris has not seemingly been identified since its original description (Underwood 1896) and its relationship to Helvella would probably require investigation.

*One of the major groups of fungi, ascomycetes produce spores in an ascus, an elongate structure with spores contained in a row within it.

A stem-less Helvella, H. astieri, photographed by Thomas Læssøe.

Members of the genus Helvella are commonly known as 'saddle fungi' or 'elfin saddles' due to the appearance of the fruiting bodies in some species. Other species possess a variety of different fruiting morphologies, some cup-like, some irregularly folded and lumpy. Not all Helvella species produce fruiting bodies supported by a stalk: in some, the fruiting body sits on the ground or remains partially submerged (Kimbrough et al. 1996), and it has been suggested that such forms may provide some indication how the truffles evolved from above-ground forms. All Helvella species fruit on soil (i.e. never on rotting wood or other such substrates) and it seems likely that all members of the Helvellaceae form ectomycorrhizal associations with plant roots (Hansen 2006).

How to spot desert truffles... (from here)

The truffle members of the Helvellaceae have a solid gleba (the spore-bearing inner mass) interspersed with veins or pockets of hymenia (the spore-producing tissues) separated by sterile tissue (Kimbrough et al. 1996). Picoa species grow in association with Helianthemum (rockrose) species and are among the 'desert truffles' collected in arid parts of the Mediterranean. They are eaten, but are not considered commercially significant due to their small size. Among Helvella species, the white saddle Helvella crispa and black saddle Helvella lacunosa have been described as edible, so long as they are cooked properly.

What the picture above may lead you to... Picoa juniperi, from here.


Hansen, K. 2006. Systematics of the Pezizomycetes—the operculate discomycetes. Mycologia 98 (6): 1029-1040.

Kimbrough, J. W., L.-T. Li & C.-G. Wu. 1996. Ultrastructural evidence for the placement of the truffle Barssia in the Helvellaceae (Pezizales). Mycologia 88 (1): 38-46.

Lumbsch, H. T., & S. M. Huhndorf (eds) 2007. Outline of Ascomycota—2007. Myconet 13: 1-58.

Percudani, R., A. Trevisi, A. Zambonelli & S. Ottonello. 1999. Molecular phylogeny of truffles (Pezizales: Terfeziaceae, Tuberaceae) derived from nuclear rDNA sequence analysis. Molecular Phylogenetics and Evolution 13 (1): 169-180.

Underwood, L. M. 1896. On the distribution of the North American Helvellales. Minnesota Botanical Studies Bulletin 9 (8): 483-500.

Patterns on a Squill

Violet squill Ledebouria socialis, photographed by Stan Shebs.

The south of Africa is one of the world's centres for botanical diversity. Home to an abundance of the floristically wierd and wonderful, you might be surprised to know just how many of your favourite garden plants (assuming that you have favourite garden plants) originate from that part of the world: proteas, leucadendrons, red-hot pokers (Kniphofia), freesias, agapanthus*... to name a few. The subject of today's post, the genus Ledebouria, is perhaps not one of the best known of the southern African contributions to horticulture, but it's none the less noteworthy.

*Well, personally, I'm not that fussed on agapanthus ('orrible weedy things), but a not insignificant number of people would disagree with me on that point.

Ledebouria revoluta, from here.

Ledebouria is a genus of the plant family Hyacinthaceae that also includes such familiar plants as hyacinths and bluebells, and within that family to a group known as squills. Like other members of the family, Ledebouria species are bulbiferous with developed leaves only present for part of the year. There are about forty or more species of Ledebouria in southern Africa, with outliers in Madagascar and India (Manning et al. 2004), though the number of species varies according to whether or not the genera Drimiopsis and Resnova are treated separately. Molecular analyses have tended to fail to distinguish the three genera, but morphological and combined analyses support their reciprocal monophyly (Lebatha et al. 2006). The Drimiopsis and Resnova species have more loosely packed leaves in the bulb than the species of Ledebouria sensu stricto (Lebatha et al. 2006) and are mostly woodland and forest species as opposed to the open-country Ledebouria (Manning et al. 2004).

Ledebouria marginata, from here.

Some species of Ledebouria have become popular as houseplants, not for their flowers which are reasonably modest, but for their leaves which are fleshy and marked with dark purple blotches and stripes. The number of leaves produced from one bulb at a time varies from up to twenty-five to only a single leaf in Ledebouria monophylla. Mature plants may be up to a metre tall in L. zebrina, down to only 3 mm high in L. galpinii (Venter 1993). The latter (as well L. monophylla) is one of a number of species in which the leaves grow tightly pressed to the ground, so despite the low height of the entire plant, the individual leaves are up to 80 mm long. In such species, the total number of leaves at a time is always low, never more than five. This growth habit is known as geophylly, and the reasons behind it remain uncertain. Geophyllous plants are generally found in areas with strongly seasonal yet regular rainfall (Esler et al. 1999). It has been suggested that the geophyllous habit protects against grazing animals or against CO2 or water loss; alternatively (as favoured by Esler et al.), it may create a microclimate that affects the temperature of the leaves, either causing their temperature to remain low in the mornings (allowing dew to form on the leaves) and/or raising the temperature of the leaves during midday (allowing elevated rates of photosynthesis).

Leaves of Ledebouria ovatifolia ssp. scabrida, a geophyllous species, photographed by Connall Oosterbroek.

As already alluded to, most Ledebouria plants form flower spikes bearing only pale flowers, though many species may produce more than one spike in succession over a single growing season. Flowers are insect-pollinated by Lepidoptera and Hymenoptera. Fruits are dry capsules, and the seeds are dispersed short distances from the parent plant by wind (generally by being scattered from a waving spike) or water (mostly by falling rain). Some species form lateral bulblets, such as the aptly named Ledebouria socialis (see this page on L. socialis as a house plant), leading to the formation of colonies of plants connected by subterranean stolons up to 200 mm long. The largest recorded such colony, for a clone of L. cooperi, had a diameter of five meeters (Venter 1993).


Esler, K. J., P. W. Rundel & P. Vorster. 1999. Biogeography of prostrate-leaved geophytes in semi-arid South Africa: hypotheses on functionality. Plant Ecology 142 (1-2): 105-120.

Lebatha, P., M. H. Buys & G. Stedje. 2006. Ledebouria, Resnova and Drimiopsis: a tale of three genera. Taxon 55 (3): 643-652.

Manning, J. C., P. Goldblatt & M. F. Fay. 2004. A revised generic synopsis of Hyacinthaceae in sub-Saharan Africa, based on molecular evidence, including new combinations and the new tribe Pseudoprospereae. Edinburgh Journal of Botany 60 (3): 533-568.

Venter, S. 1993. A revision of the genus Ledebouria Roth in South Africa. MSc thesis, University of Natal.

The Claim-Jumpers and Grave-Robbers of Taxonomy

In a recent paper in Zootaxa (openly accessible), O'Hara (2011) has become the most recent of a number of authors to discuss one of the more irritating taxonomic developments of recent years: the rise of the serial homonym replacer. A taxonomic homonym, in case you aren't already familiar with the term, is when a new taxon is given a name previously assigned to a distinct taxon (usually because the later author is unaware of the earlier usage's existence). Because the various nomenclatural codes require that any name can refer to only a single taxon, the more recently named taxon would generally need to be re-christened if it is to be accepted into polite society. However, in many cases homonymous names can lurk undetected in the literature for a great many years. After all, there is a heck of a lot of taxonomic literature out there, and it may only be a matter of luck if the existence of a homonymy is even noticed.

In recent years, this has changed somewhat. The appearance of easily searchable taxonomic databases such as Nomenclator Zoologicus have made it much easier for authors to detect if a given name has been used previously. Unfortunately, as well as making it much easier to allow authors of new taxa to avoid creating homonymies, such databases have allowed the rise of the serial homonym replacer. Serial homonym replacers scour databases on the hunt for unreformed homonyms. Having collected a bundle of them together, they then publish short papers in which they publish replacement names for said homonyms, generally in obscure little journals probably published by the authors themselves.

Most working taxonomists regard such behaviour as unlaudable at best, and as downright unethical and injurious at worst. It is felt that the publication of replacement names is best done within the context of a larger-scale review of the taxonomic group to with a homonymous name belongs. From a practical viewpoint, the publication of replacement names without putting them into a larger perspective may reduce the chance of them coming to the attention of the appropriate workers (a worker on Braconidae, for instance, will almost certainly read a paper entitled 'Taxonomic Review of the Braconidae', but may not notice potential significance in 'Five new replacement names for homonymous insect genera'), increasing the chance that they will themselves publish further, unnecessary replacement names. From an ethical viewpoint, the serial homonym replacer is, through the required practice of author citation, inflating the apparent significance of their own work and diminishing that of more exacting researchers who are forced to work more slowly.

Perhaps even more problematic, the publication of replacement names outside the context of a proper review often leads to mere compounded errors. In practice, not every junior homonym needs a replacement, because sometimes any replacement would not actually be used, and would simply clutter up the literature. If the homonym is synonymous with another previously proposed name, then that name is already available for use. For instance, the name Platypus published by Shaw in 1799 for (naturally) the platypus is a junior homonym of a genus of beetles named by Herbst in 1793. However, no replacement name is required because Blumenbach had also described the platypus in 1800 under the name Ornithorhynchus. Authors have also refrained from publishing replacement names in cases where the identity of an original homonymous name is uncertain (for instance, if the type specimens are lost): any replacement would be equally mysterious and practically unusable. In one case described by O'Hara (2011), the replacement name proposed for a genus of fly was unnecessary because the supposed 'senior homonym' had not actually met the requirements for valid publication.

In addition to the examples discussed by O'Hara (2011), let me direct your attention to one particularly horrid little paper that manages to cover many of the errors perpetrated by database scourers. Özdikmen (2009) proposed replacement names for 48 homonymous genera of unicellular eukaryotes. Let me just start by noting that Özdikmen seemed unaware that by 2009 the taxonomic concept of 'Phytomastigophorea' was more anachronistic than the ruffed collar and velvet doublet. Twelve of the supposed homonyms treated are dinoflagellates, a silicoflagellate and a chlorophyte(!), and hence members of groups whose researchers have long since generally agreed to follow the Botanical Code rather than the Zoological. Under the Botanical Code, these names are not preoccupied (because botanical names do not conflict with zoological names) and replacement is unnecessary. Even if the names were somehow problematic, I would not be surprised if the different publication requirements of the Botanical Code meant that Özdikmen's replacements were somehow not valid.

Özdikmen's (2009) proposal of a replacement name for amoeboid-endosymbiont Perkinsiella Hollande 1981 is unnecessary because a replacement name had already been published by Dyková et al. (2008), in the context of a broader molecular analysis. His proposal of a new name for the dinoflagellate family Goniodomataceae because its type genus was preoccupied is unnecessary, not only because Goniodoma is not preoccupied (see above), as family names had already been based on other genera within the Goniodomataceae and would then take precedence. Ethically speaking, many of the homonyms replaced by Özdikmen (2009) were originally published in the 1980s and 1990s and their authors are probably still alive and working today.

So what are the practical effects of this homonym harvesting? It can cause confusion and extra work for researchers, if it leads to the introduction of superfluous replacement names. It can lead to general ill will, if workers on larger projects feel that they are being unfairly pre-empted. And they can have something of a cooling effect on the very process of nomenclatural clean-up they purport to effect. Since the work of Özdikmen and his ilk became publicised, I've personally become apprehensive about the possibility of publicising, however casually, any unresolved homonyms of which I am aware.

One such homonymy I discovered nearly ten years ago, when I was fresh out of university and did not yet have any publications to my name. As the animal in question was in a group which did not then have anyone actively working on it, the idea did cross my mind that I could perhaps publish a note on it myself. My first publication! But, even at that early stage in my career, and without the benefit of mentor advice, I was able to work out that, in the end, it would be a publication of little, if any, virtue. And I hoped that I was more mature than that.


Dyková, I., I. Fiala & H. Pecková. 2008. Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): coevolution demonstrated by SSU rRNA gene phylogenies. European Journal of Protistology 44 (4): 269-277.

O'Hara, J. E. 2011. Cyber nomenclaturalists and the “CESA itch”. Zootaxa 2933: 57-64.

Özdikmen, H. 2009. Substitute names for some unicellular animal taxa (Protozoa). Munis Entomology & Zoology 4 (1): 233-256.